kate R. Jennifer O. and Anastasia A.

We used many of the resources taught to us in this seminar such as: google reader, diigo, mendeley, c map and pymol to create an interactive concept map that could be used to teach young college and high school students. This map could be used in class as a teaching tool as well as if posted to a blog site like blackboard, used as a tool for students to study or learn more about a specific topic. In this project we looked at luciferase which is a protein that catalyzes the production of light in fireflies.


Project (Thomas, Steven, Rachel)

Project aimed at integrating tools.  We want to develop a system in which a conscious stream of thought would produce keywords and tags.  These key words and tags would then be utilized in networking sites and search systems to find information of interest to the researcher.  The current set up would take input as a blog entry interpreting to tags and keywords.  Those tags and keywords would link up to similar blog entries and find links to associated information, including tools.

Would be a great tool to link colleagues, mentors and advisees up with one another.

link to presentation: Automated Research Assistant

link to example blog: https://bioquest.org/peer2011/2011/08/12/blog-example-project/


Blog Example (project)

I’m interested in finding/understanding/characterizing the underlying genetic cause(s) of autism in mice.  I’m not sure what tools and strategies I should use in order to accomplish this task.  I just think mice are really cool!


Resource/Tool Candidates:


From Mendeley:  Paper about genetically engineered autistic mice


From Diigo:  Group aimed at discussing autism


From Reader:  Reader optimized for finding news and information about autism in mammals


From PDB visualized with Pymol: (some protein thought to be involved in mouse autism)

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Wolfram Alpha

This site is pretty fun, I finally know how many licks it takes to get to the center of a tootsie pop.



WolframAlpha is a really neat tool that has alot of different and interesting information. I found out that the 30th Tuesday in 2054 is July 25 2054.


Caroline and Raphael Protein Image

2HSJ Protein Visualization: Platelet Activating Factor from Streptococcus pneumonia

We examined protein 2HSJ, a probable platelet activating factor from S. pneumonia using PyMOL visualization tools. 2HSJ is a little studied protein that functions in lipid metabolism and hydrolysis. Our measurements show protein dimensions of 104.4 Å by  66.3 Å  by 52.5 Å (as seen in Image 1). This protein has known ligand binding between amino acid residues ALA 161 and VAL 167 (shown hot pink in Image 2).   A Consurf homology comparison using BLAST shows conserved areas in the central parts of each chain. However, much of the external surface, including the known ligand binding area, is categorized as having “insufficient data.” Thus, no conclusions about active site location based on Consurf conserved regions can be draw.

Platelet Activating Factor

Measurements shown on the structure of a probable platelet activating factor of S. pneumonia.

Platelet Activating Factor

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Lipase Consurf

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ConSurf Imaging

We used Consurf to visually analyze the structural basis for our enzyme Integrase. Since Integrase is found in viruses and functions to cleave and repackage the viral DNA we were expecting much of it to be conserved, especially near the active site. Looking at both the A and B chains we found it was most conserved on the A- chain and our guess of the active site was right on key. This was a very useful tool. In the end we found that we can actually compare both the A and B chains and check out the structural basis as a whole which was highly conserved as we expected it to be.


Anna and Shalanda – PyMol Visualization of 1OAC

Using the Protein Data Bank, we located the protein 1OAC, otherwise known as copper amine oxidase of E. coli.  It is a dimer and has two active sites which are buried away from the solvent.  The enzyme has an inactive and an active form. 1OAC has a single copper ion and a covalently bonded cofactor.  The formation of this cofactor is done post-translationally by modifying a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). (Information taken from Proteopedia)  A great summary of the enzyme is available at PDBsum.  To access that information, input the PDB code for the enzyme (1OAC).

This gallery shows two images.  The first was generated in PyMol and shows the dimer chains in two different colors.  The second image, generated by Consurf, shows the conservation of the residues of chain a (purple being most conserved, blue being most variable, and yellow representing no data available).

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Gapminder and Excel

The amount of data and the number of different ways you can display it on gapminder was impressive.  It was very interesting to see all the correlations.  The excel predictions was also interesting.  I would love to see how our predictions compare with a more complicated mathematical model.

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